ArticleGenomics2020
Proteinarium: Multi-sample protein-protein interaction analysis and visualization tool.
Article in Genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
11 citing papers in PubMed, 18 citations in OpenAlex.
- Species-specific roles of cellular communication network proteins in cartilage development: A comparative study using in vitro chondrogenic models.Journal of cell communication and signaling · 2026Article
- THRESHOLD: a comprehensive transcriptomic analysis tool for evaluating gene saturation and impact in disease progression.NAR cancer · 2025Article
- Protein-Protein Interactions in Papillary and Nonpapillary Urothelial Carcinoma Architectures: Comparative Study.JMIR bioinformatics and biotechnology · 2025Article
- The Atlas of Protein-Protein Interactions in Cancer (APPIC)-a webtool to visualize and analyze cancer subtypes.NAR cancer · 2025Article
- Protein interaction explorer (PIE): a comprehensive platform for navigating protein-protein interactions and ligand binding pockets.Bioinformatics (Oxford, England) · 2024Article
- MMR Deficiency Defines Distinct Molecular Subtype of Breast Cancer with Histone Proteomic Networks.International journal of molecular sciences · 2023Article
- Identification of Heme Oxygenase-1 as a Putative DNA-Binding Protein.Antioxidants (Basel, Switzerland) · 2022Article
- From Immunohistochemistry to New Digital Ecosystems: A State-of-the-Art Biomarker Review for Precision Breast Cancer Medicine.Cancers · 2022Review
- Protein interaction networks define the genetic architecture of preterm birth.Scientific reports · 2022Article
- Overview of methods for characterization and visualization of a protein-protein interaction network in a multi-omics integration context.Frontiers in molecular biosciences · 2022Review
- Protein Network Analysis of Whole Exome Sequencing of Severe Preeclampsia.Frontiers in genetics · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 4 institutions in 1 country.
Funding
Abstract
We posit the likely architecture of complex diseases is that subgroups of patients share variants in genes in specific networks which are sufficient to give rise to a shared phenotype. We developed Proteinarium, a multi-sample protein-protein interaction (PPI) tool, to identify clusters of patients with shared gene networks. Proteinarium converts user defined seed genes to protein symbols and maps them onto the STRING interactome. A PPI network is built for each sample using Dijkstra's algorithm. Pairwise similarity scores are calculated to compare the networks and cluster the samples. A layered graph of PPI networks for the samples in any cluster can be visualized. To test this newly developed analysis pipeline, we reanalyzed publicly available data sets, from which modest outcomes had previously been achieved. We found significant clusters of patients with unique genes which enhanced the findings in the original study.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.